makeWebsite

#!/usr/bin/env python
import os
import sys
import argparse
import operator
import numpy as np
import math

names = {}
humanBed = {}
mouseBed = {}


types = ["mir_host_intron", "divergent", "sno_host", "intergenic", "mir_host_exon"]

typeToType = {
		'intergenic': 'intergenic',
		'divergent': 'divergent',
		'mir_host_intron': 'intronic miRNA host',
		'mir_host_exon': 'exonic miRNA host',
		'sno_host': 'snoRNA host',
		'coding': 'coding'
}

longname = {
		'TTI': "Transcript-Transcript Identity",
		'TGI': "Transcript-Genome Identity",
		'SSC': "Splice Site Conservation",
		'IDR': "Indel Rate"
}

TTI = {
	'mir_host_intron' : np.array([]),
	'divergent' : np.array([]),
	'sno_host' : np.array([]),
	'intergenic' : np.array([]),
	'mir_host_exon': np.array([])
}

TTIStats = {}


TGI = {
	'mir_host_intron' : np.array([]),
	'divergent' : np.array([]),
	'sno_host' : np.array([]),
	'intergenic' : np.array([]),
	'mir_host_exon': np.array([])
}

TGIStats = {}

SSC = {
	'mir_host_intron' : np.array([]),
	'divergent' : np.array([]),
	'sno_host' : np.array([]),
	'intergenic' : np.array([]),
	'mir_host_exon': np.array([])
}

SSCStats = {}


IDR = {
	'mir_host_intron' : np.array([]),
	'divergent' : np.array([]),
	'sno_host' : np.array([]),
	'intergenic' : np.array([]),
	'mir_host_exon': np.array([])
}

IDRStats = {}


colors = {
	'mir_host_intron' : "rgb(237, 145, 33)",
	'divergent' : "rgb(33, 135, 237)",
	'sno_host' : "rgb(192, 64, 160)",
	'intergenic' : "rgb(52, 158, 66)",
	'mir_host_exon': "rgb(237, 94, 33)"
}

def writeBrowse(filename, prefix):
	global TTI
	global TGI
	global SSC
	global IDR
	global REALPATH

	browse = open(prefix+'browse.html', 'w')
	
	header = open(REALPATH+'/templates/browserHeader.txt', 'r')
	for line in header.readlines():
		browse.write(line)

	f = open(filename, 'r')
	for line in f.readlines():
		if line[0]=="#": continue
		line = line.split('\t')
		
		lnc = line[0].strip()
		orth = line[2].strip()
		mAlt = line[1].strip()
		hAlt = line[3].strip()

		#get type
		if line[13].strip() == line[14].strip(): type = line[13].strip()
		else: type="intergenic"

		curTti = float(line[5].strip())
		if type in TTI: TTI[type] = np.append(TTI[type], [curTti])
		curTgi = float(line[6].strip())
		if type in TGI: TGI[type] = np.append(TGI[type], [curTgi])

		if line[8].strip() != "NA" and line[7].strip() != "NA" and float(line[8].strip()) > 0 and float(line[7].strip()) > 0:
			curIdr = math.log(float(line[7].strip()) / float(line[8].strip()), 2)
			if type in IDR: IDR[type] = np.append(IDR[type], curIdr)
		else:
			curIdr = 'NA'

		curSpliceCon = float(line[11])
		curSpliceTotal = int(line[12])
		
		if curSpliceTotal > 0: 
			if type in SSC: SSC[type] = np.append(SSC[type], [curSpliceCon / curSpliceTotal])

		mouseExons = line[9].strip()
		humanExons = line[10].strip()
		
		#write first four columns
		browse.write("<tr><td><a href=\"lnc/%s.html\" target=\"_blank\">%s</a></td><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%.2f</td><td>%.2f</td>" % (lnc, lnc, mAlt, orth, hAlt, typeToType[type], curTti, curTgi))
		
		if curIdr == "NA":
			browse.write("<td>-</td>")
		elif curIdr == 0:
			browse.write("<td>0.00</td>")
		elif curIdr > 0:
			browse.write("<td class=\"red\">%.2f</td>" % curIdr)
		elif curIdr < 0:
			browse.write("<td class=\"green\">%.2f</td>" % curIdr)

		browse.write("<td>%.1f</td><td>%d</td><td>%s</td><td>%s</td></tr>\n" % (curSpliceCon, curSpliceTotal, mouseExons, humanExons))

	footer = open(REALPATH+"templates/browserFooter.txt", 'r')

	for line in footer.readlines():
		browse.write(line)
	
	browse.close()
	f.close()

def getStats(arr):
	if len(arr) == 0:
		return [0,0,0,0,0]
	#get stats
	first = np.percentile(arr, 25)
	median = np.median(arr)
	third = np.percentile(arr, 75)

	IQR = third-first
	lower = max(np.amin(arr), first - 1.5*IQR)
	upper = min(np.amax(arr), third + 1.5*IQR)

	return [lower, first, median, third, upper]

def calculateStats():
	global TTIStats
	global TGIStats
	global SSCStats
	global IDRStats

	global types

	for type in types:
		TGIStats[type] = getStats(TGI[type])

	for type in types:
		TTIStats[type] = getStats(TTI[type])
	
	for type in types:
		SSCStats[type] = getStats(SSC[type])

	for type in types:
		IDRStats[type] = getStats(IDR[type])


def writeBox(name, x0, stats, web):
	global colors

	op = colors[name]
	trans = "rgba"+op[3:-1]+", 0.7)"

	web.write("//%s\n" % name)

	#rectangle
	web.write("{\ntype: 'rect',\nx0: %.1f,\ny0: %.2f,\nx1: %.1f,\ny1: %.2f,\n" % (x0-.3, stats[1], x0+.3, stats[3]))
	web.write("line: {\n color: '%s',\nwidth: 2\n},\nfillcolor: '%s'\n},\n" % (op, trans))
	
	#top vertical
	web.write("{\ntype: 'line', \nx0: %d,\ny0: %.2f,\tx1: %d,\ny1: %.2f,\n" % (x0, stats[3], x0, stats[4]))
	web.write("line: {\ncolor: '%s',\nwidth: 2,\ndash: 'dashdot'\n}\n}," % op)
	
	#bottom vertical
	web.write("{\ntype: 'line', \nx0: %d,\ny0: %.2f,\tx1: %d,\ny1: %.2f,\n" % (x0, stats[0], x0, stats[1]))
	web.write("line: {\ncolor: '%s',\nwidth: 2,\ndash: 'dashdot'\n}\n}," % op)

	#top horizontal
	web.write("{\ntype: 'line', \nx0: %.1f,\ny0: %.2f,\tx1: %.1f,\ny1: %.2f,\n" % (x0-.2, stats[4], x0+.2, stats[4]))
	web.write("line: {\ncolor: '%s',\nwidth: 2,\n}\n}," % op)
	
	#bottom horizontal
	web.write("{\ntype: 'line', \nx0: %.1f,\ny0: %.2f,\tx1: %.1f,\ny1: %.2f,\n" % (x0-.2, stats[0], x0+.2, stats[0]))
	web.write("line: {\ncolor: '%s',\nwidth: 2,\n}\n}," % op)

	#median
	web.write("{\ntype: 'line', \nx0: %.1f,\ny0: %.2f,\tx1: %.1f,\ny1: %.2f,\n" % (x0-.3, stats[2], x0+.3, stats[2]))
	web.write("line: {\ncolor: '%s',\nwidth: 4,\n}\n}," % op)


def writeBoxplot(name, lnc, data, lncType, stats, web):

	global types
	global longname

	web.write("<div id =\"%s\" style=\"display:inline-block\"></div>" % name)
	web.write("<script>")
	
	#write data point
	web.write("var %s = {\n" % lnc.replace("-", "").replace(".", ""))
	web.write("x: [\"intronic miRNA host\", \"divergent\", \"snoRNA host\", \"intergenic\", \"exonic miRNA host\"],\n")
	web.write("y: [%.2f, %.2f, %.2f, %.2f, %.2f],\n" % (data, data, data, data, data))
	web.write("text: ['%s', '%s', '%s', '%s', '%s'],\n" % (lnc, lnc, lnc, lnc, lnc))
	
	color = ['rgba(0, 0, 0, 0)', 'rgba(0, 0, 0, 0)', 'rgba(0, 0, 0, 0)', 'rgba(0, 0, 0, 0)', 'rgba(0, 0, 0, 0)']
	if lncType in types: color[types.index(lncType)] = 'rgba(0, 0, 0, 1)'

	colorStr = "['%s', '%s', '%s', '%s', '%s']" % (color[0], color[1], color[2], color[3], color[4])
	web.write("mode: 'markers',\nmarker: {\ncolor: %s,\nsize:10,\nsymbol:\"circle-dot\"},\n};\n" % colorStr)
	web.write("var data = [%s];" % lnc.replace("-", "").replace(".", ""))
	
	web.write("var layout = {\nxaxis: {\nrange: [-.8, 4.7],\ntype: 'category',\nshowgrid: false,\nfixedrange:true,\nshowticklabels:false\n},\n")
	web.write("yaxis: {\nrange: [0, 1.1],\nautorange:true,\nfixedrange:true\n},\nmargin: {\nt: 80,\nb:60,\nl:40,\nr:40,\npad:10\n},\nfont: {family:\"Arial, sans-serif\"},\ntitlefont: { size:16 },\nwidth: 250,\nheight: 300,\ntitle:\"%s\",\nshapes: [\n" % longname[name])

	x0 = 0
	for type in types:
		writeBox(type, x0, stats[type], web)
		x0 += 1
	
	#write data circle
	#if lncType in types: web.write("{\ntype: 'circle',\nx0: %.1f,\ny0: %.1f,\nx1: %.1f,\ny1:%.1f\n}\n" % (types.index(lncType)-.1, data-.1, types.index(lncType)+.1, data+.1))
	web.write("]\n};\nPlotly.plot('%s', data, layout, {showLink: false});\n</script>" % name)

def inExon(base, start, sizes, starts):
	for i in range(len(sizes)):
		if sizes[i] == "": continue
		#print base, (start + int(starts[i])), (start + int(starts[i]) + int(sizes[i]))
		if base >= (start + int(starts[i])) and base < (start + int(starts[i]) + int(sizes[i])):
			return True
	return False
def flip(base, start, end, hStrand, mStrand):
	if hStrand == mStrand: return base
	else: return (end - (base - start))

def scale(base, hStart, hEnd, mStart, mEnd):
	frac = (base * 1.0 - hStart) / (hEnd - hStart)
	newBase = hStart + (frac * (mEnd - mStart * 1.0))
	return newBase

#def offset(base, mStart, hStart, ratio):
#	return mStart + (base - hStart)

def writeAlignment(lnc, orth, mouse, human, maf_dir, web):
	global SPECIESA
	global SPECIESB

	mChr = mouse[0].strip()
	mStart = int(mouse[1])
	mEnd = int(mouse[2])
	mStrand = mouse[5].strip()
	mNumExons = int(mouse[9])
	mExonSizes = mouse[10].split(",")
	mExonStarts = mouse[11].split(",")

	hChr = human[0].strip()
	hStart = int(human[1])
	hEnd = int(human[2])
	hStrand = human[5].strip()
	hNumExons = int(human[9])
	hExonSizes = human[10].split(",")
	hExonStarts = human[11].split(",")

	offset = mStart - hStart

	if not os.path.exists("%s/%s-%s.maf" % (maf_dir, lnc, orth)): return

	maffile = open("%s/%s-%s.maf" % (maf_dir, lnc, orth))
	counter = 0
	for line in maffile.readlines():
		if line[0] == "#": continue
		if counter == 0:
			score = line.split()
		elif counter == 1:
			mousemaf = line.split()
		elif counter == 2:
			humanmaf = line.split()
		else:
			break
		counter += 1
	if counter == 0: return

	web.write("<div id=\"align\" style=\"width;500px;height:500px;\"></div>\n")
	web.write("<script>\n")
	
	mSize = int(mouse[2]) - int(mouse[1])	
	hSize = int(human[2]) - int(human[1])
	
	if mSize > hSize: hSize = mSize

	#print hSize, int(mouse[2]), int(mouse[1])+hSize
	#write mouse axis
	web.write("var trace2 = {\ny:[1.7, 1.7],\nx:[%d,%d],\nmode: 'lines',\nline: {\ncolor:\"rgba(255,255,255,0)\"\n},\nxaxis: 'x2',\nshowlegend:false,\nhoverinfo:\"none\"};\n" % (int(mouse[1]), int(mouse[1])+hSize))

	#write human axis
	web.write("var trace1 = {\ny:[1.3, 1.3],\nx:[%d,%d],\nmode: 'lines',\nline: {\ncolor:\"rgba(255,255,255,0)\"\n},\nshowlegend:false,\nhoverinfo:\"none\"};\n" % (hStart, hStart+hSize))

	web.write("var data = [trace1, trace2];\n")

	web.write("var layout={\n")
	web.write("yaxis: {\nshowticklabels:false,\nshowgrid:false,\nrange: [1.1, 1.9]}\n,\n")
	if hStrand == "-": web.write("xaxis: {title:'<em>%s</em><br><br>%s',\nrange: [%d, %d],\nexponentformat:\"none\",\nshowgrid:false,\ntitlefont: {size:18\n},\n},\n" % (hChr, SPECIESB, hStart + hSize, hStart))
	else: web.write("xaxis: {title:'<em>%s</em><br><br>%s',\nexponentformat:\"none\",\nshowgrid:false,\ntitlefont: {size:18}\n},\n" % (hChr, SPECIESB))
	if mStrand == "-": web.write("xaxis2: {\ntitle: '%s<br><br><em>%s</em>',\nrange: [%d, %d],\noverlaying: 'x',\nside: 'top',autorange:true,\nexponentformat:\"none\",\ntitlefont: {size:18\n},\n},\n" % (SPECIESA, mChr, mStart + hSize, mStart))
	else: web.write("xaxis2: {\ntitle: '%s<br><br><em>%s</em>',\noverlaying: 'x',\nside: 'top',autorange:true,\nexponentformat:\"none\",\ntitlefont: {size:18}\n},\n" % (SPECIESA, mChr))
	web.write("margin: {\nb:110,\nt:110\n},\n")
	web.write("shapes: [\n")


	if mStrand == "+": mBase = int(mousemaf[2])-1
	else: 
		mSrcSize = int(mousemaf[5])
		mBase = mSrcSize - int(mousemaf[2])-1 
	if hStrand == "+": hBase = int(humanmaf[2])-1
	else: 
		hSrcSize = int(humanmaf[5])
		hBase = hSrcSize - int(humanmaf[2])-1

	mStr = mousemaf[6]
	hStr = humanmaf[6]
	curMStr = ""
	curHStr = ""
	
	if mStrand == "+": mStrand = 1
	else: mStrand = -1
	
	if hStrand == "+": hStrand = 1
	else: hStrand = -1


	for i in range(len(mousemaf[6].strip())):
		if mBase >= mStart and hBase >= hStart and mBase < mEnd and hBase < hEnd:
			
			if mStr[i].upper() == hStr[i].upper():
				curMStr += mStr[i]
				curHStr += hStr[i]
				#if mBase >= 31300140 and mBase < 31300200:
				#	print mBase, inExon(mBase, mStart, mExonSizes, mExonStarts), curMStr, curHStr, hBase, inExon(hBase, hStart, hExonSizes, hExonStarts)
				#	print hBase, hStart, hExonSizes, hExonStarts
			else:
				if len(curMStr) > 0:
					lenMStr = len(curMStr) * mStrand
					lenHStr = len(curHStr) * hStrand 
					#if mBase > 31300140 and mBase < 31300200:
					#	print "draw!", 
#						print "   from", mBase+(mStrand*-1), mBase+(mStrand*-1), inExon(mBase+(mStrand*-1), mStart, mExonSizes, mExonStarts), inExon(mBase+(mStrand*-1), mStart, mExonSizes, mExonS
#						print "   to", mBase-lenMStr, hBase-lenHStr, inExon(mBase-lenMStr, mStart, mExonSizes, mExonStarts), inExon(hBase-lenHStr, hStart, hExonSizes, hExonStarts)
					
					if inExon(mBase+(mStrand*-1), mStart, mExonSizes, mExonStarts) and inExon(hBase+(hStrand*-1), hStart, hExonSizes, hExonStarts):
						#if aligned region all in exon
						if (inExon(mBase-lenMStr, mStart, mExonSizes, mExonStarts) and inExon(hBase-lenHStr, hStart, hExonSizes, hExonStarts)) :
							#print hBase+(hStrand*-1) + (hStrand == 1), hBase-lenHStr + (hStrand == -1), curHStr, "exon"
							web.write("{\ntype:'path',\npath: ' M %d,1.6 L%d,1.6 L%d,1.4 L%d,1.4 Z',\n xref: 'x2',\n fillcolor: 'rgb(249,197,200)',\nline: {\ncolor: 'rgb(249,197,200)',\nwidth: 1\n},\n},\n" % (mBase-lenMStr+ (mStrand == -1), mBase+(mStrand*-1) + (mStrand == 1), flip(hBase+(hStrand*-1) + (hStrand == 1) + offset, mStart, mStart+hSize, hStrand, mStrand), flip(hBase-lenHStr + (hStrand == -1)+ offset, mStart, mStart+hSize, hStrand, mStrand)))
						else:
							a = mBase - lenMStr
							b = hBase - lenHStr
							
							if lenMStr > 0:
								for x in range(lenMStr):
									if (inExon(a+x, mStart, mExonSizes, mExonStarts) and inExon(b+(x*mStrand*hStrand), hStart, hExonSizes, hExonStarts)):
										break
							else:
								for x in range(0, lenMStr, -1):
									if (inExon(a+x, mStart, mExonSizes, mExonStarts) and inExon(b+(x*mStrand*hStrand), hStart, hExonSizes, hExonStarts)):
										break
							splitA = a+x
							splitB = b+(x*mStrand*hStrand)

							#write intron-exon
							web.write("{\ntype:'path',\npath: ' M %d,1.6 L%d,1.6 L%d,1.4 L%d,1.4 Z',\n xref: 'x2',\n fillcolor: 'rgb(198,215,247)',\nline: {\ncolor: 'rgb(198,215,247)',\nwidth: 1\n},\n},\n" % (mBase-lenMStr + (mStrand == -1), splitA + (mStrand*-1) + (mStrand == 1), flip(splitB + (hStrand*-1) + (hStrand ==1)+offset, mStart, mStart+hSize, hStrand, mStrand), flip(hBase-lenHStr + (hStrand==-1) + offset, mStart, mStart+hSize, hStrand, mStrand)))
							web.write("{\ntype:'path',\npath: ' M %d,1.6 L%d,1.6 L%d,1.4 L%d,1.4 Z',\n xref: 'x2',\n fillcolor: 'rgb(249,197,200)',\nline: {\ncolor: 'rgb(249,197,200)',\nwidth: 1\n},\n},\n" % (splitA + (mStrand == -1), mBase + (mStrand*-1) + (mStrand==1), flip(hBase + (hStrand*-1) + (hStrand==1) +offset, mStart, mStart+hSize, hStrand, mStrand), flip(splitB + (hStrand == -1)+offset, mStart, mStart+hSize, hStrand, mStrand)))


					else:
						if not inExon(mBase-lenMStr, mStart, mExonSizes, mExonStarts) or not inExon(hBase-lenHStr, hStart, hExonSizes, hExonStarts):

							web.write("{\ntype:'path',\npath: ' M %d,1.6 L%d,1.6 L%d,1.4 L%d,1.4 Z',\n xref: 'x2',\n fillcolor: 'rgb(198,215,247)',\nline: {\ncolor: 'rgb(198,215,247)',\nwidth: 1\n},\n},\n" % (mBase-lenMStr + (mStrand == -1), mBase+(mStrand*-1) + (mStrand == 1), flip(hBase+(hStrand*-1) + (hStrand == 1)+offset, mStart, mStart+hSize, hStrand, mStrand), flip(hBase-lenHStr + (hStrand == -1)+offset, mStart, mStart+hSize, hStrand, mStrand)))

						#split exon-intron
						
						else:
							
						
							a = mBase-lenMStr
							b = hBase-lenHStr
							
							if lenMStr > 0:
								for x in range(lenMStr):
									if not (inExon(a+x, mStart, mExonSizes, mExonStarts) and inExon(b+ (x * mStrand * hStrand), hStart, hExonSizes, hExonStarts)):
										break
							else:
								for x in range(0, lenMStr, -1):
									if not (inExon(a+x, mStart, mExonSizes, mExonStarts) and inExon(b+(x*mStrand*hStrand), hStart, hExonSizes, hExonStarts)):
										break
							
							splitA = a+x
							splitB = b+(x*mStrand*hStrand)
							
							web.write("{\ntype:'path',\npath: ' M %d,1.6 L%d,1.6 L%d,1.4 L%d,1.4 Z',\n xref: 'x2',\n fillcolor: 'rgb(249,197,200)',\nline: {\ncolor: 'rgb(249,197,200)',\nwidth: 1\n},\n},\n" % (mBase-lenMStr + (mStrand==-1), splitA + (mStrand*-1) + (mStrand == 1), flip(splitB + (hStrand*-1) + (hStrand==1)+offset, mStart, mStart+hSize, hStrand, mStrand), flip(hBase-lenHStr+(hStrand==-1)+offset, mStart, mStart+hSize, hStrand, mStrand)))
							web.write("{\ntype:'path',\npath: ' M %d,1.6 L%d,1.6 L%d,1.4 L%d,1.4 Z',\n xref: 'x2',\n fillcolor: 'rgb(198,215,247)',\nline: {\ncolor: 'rgb(198,215,247)',\nwidth: 1\n},\n},\n" % (splitA + (mStrand == -1), mBase+(mStrand*-1) + (mStrand==1), flip(hBase+(hStrand*-1) + (hStrand==1)+offset, mStart, mStart+hSize, hStrand, mStrand), flip(splitB + (hStrand==-1)+offset, mStart, mStart+hSize, hStrand, mStrand)))


					curMStr = ""
					curHStr = ""
	
		if mStr[i] != "-": 
			if mStrand == 1: mBase += 1
			else: mBase -= 1
		if hStr[i] != "-": 
			if hStrand == 1: hBase += 1
			else: hBase -=1
	
	for i in range(mNumExons):
		start = mStart + int(mExonStarts[i])
		end = start + int(mExonSizes[i])
		web.write("{\ntype: 'rect',\n x0: %d,\n y0: 1.6,\n x1: %d,\n y1: 1.8,\n xref: 'x2',\n line: {\n color: 'rgb(127, 127, 127)',\nwidth: 2\n},\nfillcolor: 'rgb(127, 127, 127)'\n},\n" %(start, end))
	web.write("{\ntype: 'line',\n x0: %d,\n y0: 1.7,\n x1: %d,\n y1: 1.7,\n xref: 'x2',\n line: {\n color: 'rgb(127, 127, 127)',\nwidth: 2\n}\n},\n" %(mStart, mEnd))
	for i in range(hNumExons):
		start = hStart + int(hExonStarts[i])
		end = start + int(hExonSizes[i])
		#web.write("{\ntype: 'rect',\n x0: %d,\n y0: 1.2,\n x1: %d,\n y1: 1.4,\n xref: 'x',\n line: {\n color: 'rgb(127, 127, 127)',\nwidth: 2\n},\nfillcolor: 'rgb(127, 127, 127)'\n},\n" %(start, end))
		web.write("{\ntype: 'rect',\n x0: %d,\n y0: 1.2,\n x1: %d,\n y1: 1.4,\n xref: 'x2',\n line: {\n color: 'rgb(127, 127, 127)',\nwidth: 2\n},\nfillcolor: 'rgb(127, 127, 127)'\n},\n" %(flip(start+offset, mStart, mStart+hSize, mStrand, hStrand), flip(end+offset, mStart, mStart+hSize, mStrand, hStrand)))
	web.write("{\ntype: 'line',\n x0: %d,\n y0: 1.3,\n x1: %d,\n y1: 1.3,\n xref: 'x',\n line: {\n color: 'rgb(127, 127, 127)',\nwidth: 2\n}\n},\n" %(hStart, hEnd))

#	print numBlocks
	web.write("]\n};\n")
	web.write("Plotly.newPlot('align', data, layout, {showLink: false});\n")
	web.write("</script>\n")


def writeEachLnc(filename, human, mouse, maf_dir, prefix):
	global humanBed
	global mouseBed

	for line in human.readlines():
		splitline = line.split()
		lncName = splitline[3].strip()
		humanBed[lncName] = splitline

	for line in mouse.readlines():
		splitline = line.split()
		lncName = splitline[3].strip()
		mouseBed[lncName] = splitline


	f = open(filename, 'r')
	for line in f.readlines():
		if line[0]=="#": continue
		line = line.split('\t')
		
		lnc = line[0].strip()
		orth = line[2].strip()
		mAlt = line[1].strip()
		hAlt = line[3].strip()

		#get type
		if line[13].strip() == line[14].strip(): type = line[13].strip()
		else: type="intergenic"

		curTti = float(line[5].strip())
		curTgi = float(line[6].strip())

		if line[8].strip() != "NA" and line[7].strip() != "NA" and float(line[8].strip()) > 0 and float(line[7].strip()) > 0:
			curIdr = math.log(float(line[7].strip()) / float(line[8].strip()), 2)
			if type in IDR: IDR[type] = np.append(IDR[type], curIdr)
		else:
			curIdr = 'NA'

		curSpliceCon = float(line[11])
		curSpliceTotal = int(line[12])
	
		head = open(REALPATH+"templates/lncPageHeader.txt", 'r')
		lncPage = open(prefix+"/lnc/"+lnc+".html", 'w')

		for line in head.readlines():
			lncPage.write(line)

		global SPECIESA
		global SPECIESB

		lncPage.write("<h1>%s</h1><hr>\n" % lnc)
		lncPage.write("<a href=\"http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s%%3A%s-%s\" target=\"_blank\">UCSC (%s) <img src=\"http://www.southcypress.com/site/images/graphics/icons/icon-new-window.gif\"></a>\n" % (SPECIESA, mouseBed[lnc][0], mouseBed[lnc][1], mouseBed[lnc][2], SPECIESA))
		lncPage.write("&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s%%3A%s-%s\" target=\"_blank\">UCSC (%s) <img src=\"http://www.southcypress.com/site/images/graphics/icons/icon-new-window.gif\"></a>\n" % (SPECIESB, humanBed[orth][0], humanBed[orth][1], humanBed[orth][2], SPECIESB))
		lncPage.write("<br><br><h4>Alignment</h4><hr>\n")
		writeAlignment(lnc, orth, mouseBed[lnc], humanBed[orth], maf_dir, lncPage)
		
		lncPage.write("<br><br><h4>Evolutionary Metrics</h4><hr>\n")
		writeBoxplot("TGI", lnc, curTgi, type, TGIStats, lncPage)
		writeBoxplot("TTI", lnc, curTti, type, TTIStats, lncPage)
		if curSpliceTotal > 0: 
			curSsc = curSpliceCon / curSpliceTotal
			writeBoxplot("SSC", lnc, curSsc, type, SSCStats, lncPage)
		if curIdr != "NA":
			writeBoxplot("IDR", lnc, curIdr, type, IDRStats, lncPage)

REALPATH = ""
SPECIESA = ""
SPECIESB = ""

ALLLNCS = set()

def main():
	parser = argparse.ArgumentParser(description='makeWebsite')
	parser.add_argument('file', type=str, help='file')
	parser.add_argument('specA', type=str)
	parser.add_argument('specB', type=str)
	parser.add_argument('mouse_bed', type=file)
	parser.add_argument('human_bed', type=file)
	parser.add_argument('maf_dir', type=str)
	parser.add_argument('prefix', type=str)
	args = parser.parse_args()
	
	global REALPATH
	REALPATH = os.path.realpath(__file__)[0:-11]
	
	global SPECIESA
	global SPECIESB
	SPECIESA = args.specA
	SPECIESB = args.specB

	writeBrowse(args.file, args.prefix)
	calculateStats()

	if not os.path.exists(args.prefix+"lnc/"): os.system("mkdir %s/lnc" % args.prefix)
	writeEachLnc(args.file, args.human_bed, args.mouse_bed, args.maf_dir, args.prefix)


if __name__ == "__main__":
	main()